ok thank you very much. i will try and get back to u
regards
divya
On 11 July 2013 14:26, Dr. Vitaly Chaban wrote:
> Indeed.
>
>
> So, go to your main topology file and define a new atom type "Xe" under an
> appropriate section. Then just add sigma and epsilon in the non-bonded
> section and y
Indeed.
So, go to your main topology file and define a new atom type "Xe" under an
appropriate section. Then just add sigma and epsilon in the non-bonded
section and you are ready to explore the binding.
Dr. Vitaly V. Chaban
On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil wrote:
> ya.. but t
ya.. but there is experimental data to confirm the presence. can you help
me to solve this problem
On 9 July 2013 11:54, Dr. Vitaly Chaban wrote:
> Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will
> obviously not sit in the binding site
>
>
> Dr. Vitaly V. Chaban
>
>
Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will
obviously not sit in the binding site
Dr. Vitaly V. Chaban
On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil wrote:
> thanks for the reply.. I am planning to place Xe in the protein binding
> site ( just like a metal atom).
thanks for the reply.. I am planning to place Xe in the protein binding
site ( just like a metal atom). I made a topology file with xe charge and
mass. I have two options to implement the simulation. 1. like
protein-ligand simulation. 2. replacing a number of solvent (water)
molecules with xe in th
I am a too curious person not to ask WHY Xe is of interest in connection
with the protein..?
Dr. Vitaly V. Chaban
On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul wrote:
>
>
> On 7/8/13 9:21 AM, divyasunil wrote:
>
>> Hello,
>>
>> Please help me to add Xe atom to GROMOS96 53a6 force field. I nee
On 7/8/13 9:21 AM, divyasunil wrote:
Hello,
Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry
out a protein-Xe simulation . I tried myself but failed.
Parameterization is an expert topic and requires considerable time and effort.
If there are existing parameters t
Hello,
Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry
out a protein-Xe simulation . I tried myself but failed.
Thanks and Regards
Divya
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